refactor: dump all data export functionality from xcms

[jorainer]

• Remove the data export functionality (saveResults()) from xcms as it will be implemented (in a more structured and cleaner way) in the new MsIO package.

Advantage:

• development can be done independently of xcms and Bioconductor release cycles.
• have export/import methods not only for the xcms objects, but all other related ones (Spectra, MsBackend, MsExperiment, ...).
• less package dependencies in xcms

Disadvantage:

• I removed the exported methods and classes from xcms - but I don't think anybody was already using them.

[sneumann]

• I am not sold on the independence from BioC releases, if MsIO one day goes Bioc ...
• the dependency bloat will then be in MsIO which then depends on a slew of packages like xcms, Spectra, ... But I don't see a way out of that. An advantage could be that we can combine e.g. xcms + Spectra into mzTab.

[jorainer]

I am not sold on the independence from BioC releases, if MsIO one day goes Bioc ...

sorry, was maybe not clear there. This is just for the short-term of course. We're currently experimenting and evaluating different export/import ways, so I just think we don't have a final version implemented until September (for the BioC release). Thus, it would be for now safer to use the MsIO package as a playground and don't risk having unfinished code in xcms (for the release).

Also, import/export of xcms result objects would make sense in xcms, true, but the xcms objects extend MsExperiment, Spectra etc objects. so, having the import/export of these objects in xcms is not good. and splitting them across the respective packages is also not ideal, especially because some code is shared (e.g. the "Param" classes and the import/export methods). Thus, we bundle them at the moment in the MsIO package - if it's settled we might decide to distribute the final functionality into the respective packages - but it has also advantages (mostly for maintainence) to keep all in one place.

For the dependency bloat - for now we have MsExperiment, Spectra, xcms "only" in Suggests, but not in imports. So, MsIO is quite "lean" to install. To import/export e.g. a xcms result object it is anyway required to (install and) load the xcms package FIRST, so, we don't have (at least as it looks now) any issues.

So, for now we're re-implementing the "plain text file" import/export in MsIO - in a cleaner way that we did in xcms (which e.g. supported only Spectra with an MsBackendMzR backend). Then, we're also playing with adding support for alabaster, Bioconductor's new way to save R objects in a language agnostic format.

So, to summarize: for now I would like to remove the old import/export code from xcms and have it implemented in a cleaner way in MsIO. Maybe later (for the next BioC release) we can bring it back into xcms - but I also see an advantage in having that functionality separately for ease of maintenance and bundling of similar functionality within a single package.

[sneumann]

Yes, looks good to me. R CMD check also works locally. Yours, Steffen